SQANTI3 Analysis: complete transcriptome

Reference
Reference: Shared reference drawing used for all categories.
Isoform (FSM)
FSM (Full Splice Match): The reference and query isoform have the same number of exons and each internal junction agree. The exact 5' start and 3' end can differ by any amount.
Isoform (ISM)
ISM (Incomplete Splice Match): The query isoform has fewer 5' exons than the reference, but each internal junction agree. The exact 5' start and 3' end can differ by any amount.
Isoform (NIC)
NIC (Novel In Catalog): The query isoform does not have a FSM or ISM match, but is using a combination of known donor/acceptor sites.
New SiteIsoform (NNC)
NNC (Novel Not in Catalog): The query isoform does not have a FSM or ISM match, and has at least one donor or acceptor site that is not annotated.
OverlapIsoform (Genic)
Genic Genomic: The query isoform overlaps with introns and exons.
Isoform (-)
Antisense: The query isoform does not overlap a same-strand reference gene but is anti-sense to an annotated gene.
Isoform (Fusion)
Fusion: The query isoform spans two or more annotated genes.
Isoform (Inter)
Intergenic: The query isoform is in the intergenic region.
Isoform (Intron)
Genic Intron: The query isoform is completely contained within an annotated intron.

Structural Categories: All structural categories and definitions are shown below.

For more details on categories, visit here: SQANTI3 Wiki: Categories.
For a detailed explanation of each column of the table (SQANTI3 classification), see here: Column Glossary.


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Total transcripts: 29903 | Close Window

isoformchromstrandlengthexonsstructural_categoryassociated_geneassociated_transcriptref_lengthref_exonsdiff_to_TSSdiff_to_TTSdiff_to_gene_TSSdiff_to_gene_TTSsubcategoryRTS_stageall_canonicalmin_sample_covmin_covmin_cov_possd_covFLn_indelsn_indels_juncbiteiso_expgene_expratio_expFSM_classcodingORF_lengthCDS_lengthCDS_startCDS_endCDS_genomic_startCDS_genomic_endpredicted_NMDperc_A_downstream_TTSseq_A_downstream_TTSdist_to_CAGE_peakwithin_CAGE_peakdist_to_polyA_sitewithin_polyA_sitepolyA_motifpolyA_distpolyA_motif_foundratio_TSS
isoformchromstrandlengthexonsstructural_categoryassociated_geneassociated_transcriptref_lengthref_exonsdiff_to_TSSdiff_to_TTSdiff_to_gene_TSSdiff_to_gene_TTSsubcategoryRTS_stageall_canonicalmin_sample_covmin_covmin_cov_possd_covFLn_indelsn_indels_juncbiteiso_expgene_expratio_expFSM_classcodingORF_lengthCDS_lengthCDS_startCDS_endCDS_genomic_startCDS_genomic_endpredicted_NMDperc_A_downstream_TTSseq_A_downstream_TTSdist_to_CAGE_peakwithin_CAGE_peakdist_to_polyA_sitewithin_polyA_sitepolyA_motifpolyA_distpolyA_motif_foundratio_TSS